Back to Workflows build report for BioC 3.14

This page was generated on 2022-04-11 21:00:10 -0400 (Mon, 11 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4323
riesling1Windows Server 2019 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4108
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4136
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD results for proteomics on riesling1


To the developers/maintainers of the proteomics package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 19/29HostnameOS / ArchINSTALLBUILD
proteomics 1.18.0  (landing page)
Laurent Gatto
Snapshot Date: 2022-04-11 14:45:01 -0400 (Mon, 11 Apr 2022)
git_url: https://git.bioconductor.org/packages/proteomics
git_branch: RELEASE_3_14
git_last_commit: c5535b5
git_last_commit_date: 2021-10-26 11:15:44 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  
riesling1Windows Server 2019 Standard / x64  OK    ERROR  
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  

Summary

Package: proteomics
Version: 1.18.0
Command: chmod a+r proteomics -R && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD build --keep-empty-dirs --no-resave-data proteomics
StartedAt: 2022-04-11 15:06:44 -0400 (Mon, 11 Apr 2022)
EndedAt: 2022-04-11 15:07:37 -0400 (Mon, 11 Apr 2022)
EllapsedTime: 52.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r proteomics -R && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD build --keep-empty-dirs --no-resave-data proteomics
###
##############################################################################
##############################################################################


* checking for file 'proteomics/DESCRIPTION' ... OK
* preparing 'proteomics':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'proteomics.Rmd' using rmarkdown
Warning: replacing previous import 'MSnbase::plot' by 'graphics::plot' when loading 'RforProteomics'

This is the 'RforProteomics' version 1.32.0.

  To get started, visit
    http://lgatto.github.com/RforProteomics/

  or, in R, open package vignettes by typing
    RforProteomics() # R/Bioc for proteomics overview
    RProtVis()       # R/Bioc for proteomics visualisation

  For a full list of available documents:
    vignette(package='RforProteomics')



Attaching package: 'RforProteomics'

The following object is masked from 'package:stats':

    spectrum

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CopyNumberVariants
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NoViewProvided
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NoViewProvided
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ConnectTools, HighThroughputSequencing
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Systems Biology, Pathway
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Bioinformatics
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Cancer
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Network Inference
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Statistics, Bioinformatics
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CopyNumber
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DataImport 
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SNPsAndGeneticVariability
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3' end sequencing, polyadenylation site, internal priming
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NoViewProvided
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CopyNumber, Mutations, Diagnosis, metastasis
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Bioinformatics
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Clustering.
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GeneticsCellBiology
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HighThroughputSequencing, HighThroughputSequencingData, Bioinformatics, MultipleComparisons
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NoViewProvided
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Bioinformatics, Cancer, FlowCytData, DensityGating
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Gating
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GraphsAndNetworks
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NaturalLanguageProcessing
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Bioinformatics
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Bioinformatics
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HighThroughputSequencing
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Biological Question
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Bioinformatics, MultipleComparisons
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NoViewProvided
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Statistical Method
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Cancer
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RNA-Seq, Differential Expression
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Bioinformatics, Statistics, MultipleComparisons
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NoViewProvided
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AMDIS, GCMS
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Bioinformatics
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HighThroughputSequencingData
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NoViewProvided
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GraphsAndNetwork
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Statistics
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NoViewProvided
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Infastructure
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PathBank, Panther
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R.utils
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NoViewProvided
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HTA2.0
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MultipleComparisons
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HighThroughputSequencing
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Bioinformatics
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HighThroughputSequencing
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NetworkAnalysis, GraphsAndNetworks
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Cancer, StemCells, HIV
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Experiment Data, Sequencing Data
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NoViewProvided
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Machine Learning, QC-RFSC, QC-RLSC, ComBat
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Regulation, HighThroughputSequencing, MultipleComparisons, Bioinformatics
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HighThroughputSequencing
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CopyNumberVariants
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NoViewProvided
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NoViewProvided
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ConnectTools, HighThroughputSequencing
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Systems Biology, Pathway
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Bioinformatics
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Cancer
Warning: Dropping unknown biocViews terms:
Network Inference
Warning: Dropping unknown biocViews terms:
Statistics, Bioinformatics
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CopyNumber
Warning: Dropping unknown biocViews terms:
DataImport 
Warning: Dropping unknown biocViews terms:
SNPsAndGeneticVariability
Warning: Dropping unknown biocViews terms:
3' end sequencing, polyadenylation site, internal priming
Warning: Dropping unknown biocViews terms:
NoViewProvided
Warning: Dropping unknown biocViews terms:
CopyNumber, Mutations, Diagnosis, metastasis
Warning: Dropping unknown biocViews terms:
Bioinformatics
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Clustering.
Warning: Dropping unknown biocViews terms:
GeneticsCellBiology
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HighThroughputSequencing, HighThroughputSequencingData, Bioinformatics, MultipleComparisons
Warning: Dropping unknown biocViews terms:
NoViewProvided
Warning: Dropping unknown biocViews terms:
NoViewProvided
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Bioinformatics, Cancer, FlowCytData, DensityGating
Warning: Dropping unknown biocViews terms:
Gating
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GraphsAndNetworks
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NaturalLanguageProcessing
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Bioinformatics
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Bioinformatics
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NoViewProvided
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HighThroughputSequencing
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NoViewProvided
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Biological Question
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Bioinformatics, MultipleComparisons
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NoViewProvided
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Statistical Method
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Cancer
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RNA-Seq, Differential Expression
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Bioinformatics, Statistics, MultipleComparisons
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NoViewProvided
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AMDIS, GCMS
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Bioinformatics
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HighThroughputSequencingData
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NoViewProvided
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GraphsAndNetwork
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Statistics
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NoViewProvided
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Infastructure
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PathBank, Panther
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R.utils
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NoViewProvided
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HTA2.0
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MultipleComparisons
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HighThroughputSequencing
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Bioinformatics
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HighThroughputSequencing
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NetworkAnalysis, GraphsAndNetworks
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Cancer, StemCells, HIV
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Experiment Data, Sequencing Data
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NoViewProvided
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Machine Learning, QC-RFSC, QC-RLSC, ComBat
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Regulation, HighThroughputSequencing, MultipleComparisons, Bioinformatics
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HighThroughputSequencing
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Quitting from lines 186-189 (proteomics.Rmd) 
Error: processing vignette 'proteomics.Rmd' failed with diagnostics:
bfcadd() failed; see warnings()
--- failed re-building 'proteomics.Rmd'

SUMMARY: processing the following file failed:
  'proteomics.Rmd'

Error: Vignette re-building failed.
Execution halted